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Cytokine PDB id
1lv9
Jmol
Contents
Protein chain
64 a.a. *
* Residue conservation analysis
PDB id:
1lv9
Name: Cytokine
Title: Cxcr3 binding chemokine ip-10/cxcl10
Structure: Small inducible cytokine b10. Chain: a. Synonym: cxcl10, interferon-gamma induced protein, gamma- ip10, ip-10. Engineered: yes
Source: Synthetic: yes. Other_details: the sequence of the protein is naturally found in homo sapiens. It was synthesized by stepwise solid phase methods using t-butoxycarbonyl protection chemistry.
NMR struc: 10 models
Authors: V.Booth,D.W.Keizer,M.B.Kamphuis,I.Clark-Lewis,B.D.Sykes
Key ref:
V.Booth et al. (2002). The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions. Biochemistry, 41, 10418-10425. PubMed id: 12173928 DOI: 10.1021/bi026020q
Date:
27-May-02     Release date:   18-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02778  (CXL10_HUMAN) -  C-X-C motif chemokine 10
Seq:
Struc: 		98 a.a.
64 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     immune response   20 terms 
  Biochemical function     receptor binding     4 terms  

 

 
DOI no: 10.1021/bi026020q Biochemistry 41:10418-10425 (2002)
PubMed id: 12173928  
 
 
The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions.
V.Booth, D.W.Keizer, M.B.Kamphuis, I.Clark-Lewis, B.D.Sykes.
 
  ABSTRACT  
 
The structure of IP-10 was solved by NMR spectroscopy and represents the first structure from the class of agonists toward the receptor CXCR3. CXCR3 binding chemokines are unique in their ability to bind receptors from both the CC and CXC classes of chemokine receptors. An unusual structural feature of IP-10 was identified that may provide the basis for the ability of IP-10 to bind both CXCR3 and CCR3. The surface of IP-10 that interacts with the N-terminus of CXCR3 was defined by monitoring changes in the NMR spectrum of IP-10 upon addition of a CXCR3 N-terminal peptide. These studies indicated that the interaction involves a hydrophobic cleft, formed by the N-loop and 40s-loop region of IP-10, similar to the interaction surface observed for other chemokines such as IL-8. An additional region of interaction was observed that consists of a hydrophobic cleft formed by the N-terminus of IP-10 and 30s-loop of IP-10.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21223963 C.L.Salanga, and T.M.Handel (2011).
Chemokine oligomerization and interactions with receptors and glycosaminoglycans: the role of structural dynamics in function.
  Exp Cell Res, 317, 590-601.  
20377877 B.H.Cheng, Y.Liu, X.Xuei, C.P.Liao, D.Lu, M.E.Lasbury, P.J.Durant, and C.H.Lee (2010).
Microarray studies on effects of Pneumocystis carinii infection on global gene expression in alveolar macrophages.
  BMC Microbiol, 10, 103.  
19274094 A.Egesten, A.I.Olin, H.M.Linge, M.Yadav, M.Mörgelin, A.Karlsson, and M.Collin (2009).
SpeB of Streptococcus pyogenes differentially modulates antibacterial and receptor activating properties of human chemokines.
  PLoS ONE, 4, e4769.  
19681642 A.Ravindran, P.R.Joseph, and K.Rajarathnam (2009).
Structural basis for differential binding of the interleukin-8 monomer and dimer to the CXCR1 N-domain: role of coupled interactions and dynamics.
  Biochemistry, 48, 8795-8805.  
19131211 D.B.Njoku, Z.Li, J.L.Mellerson, R.Sharma, M.V.Talor, N.Barat, and N.R.Rose (2009).
IP-10 protects while MIP-2 promotes experimental anesthetic hapten - induced hepatitis.
  J Autoimmun, 32, 52-59.  
19187771 F.T.Schulthess, F.Paroni, N.S.Sauter, L.Shu, P.Ribaux, L.Haataja, R.M.Strieter, J.Oberholzer, C.C.King, and K.Maedler (2009).
CXCL10 impairs beta cell function and viability in diabetes through TLR4 signaling.
  Cell Metab, 9, 125-139.  
19578117 J.Hol, A.M.Küchler, F.E.Johansen, B.Dalhus, G.Haraldsen, and I.Oynebråten (2009).
Molecular requirements for sorting of the chemokine interleukin-8/CXCL8 to endothelial Weibel-Palade bodies.
  J Biol Chem, 284, 23532-23539.  
19470579 R.J.Bodnar, C.C.Yates, M.E.Rodgers, X.Du, and A.Wells (2009).
IP-10 induces dissociation of newly formed blood vessels.
  J Cell Sci, 122, 2064-2077.  
18645041 T.Loos, A.Mortier, M.Gouwy, I.Ronsse, W.Put, J.P.Lenaerts, J.Van Damme, and P.Proost (2008).
Citrullination of CXCL10 and CXCL11 by peptidylarginine deiminase: a naturally occurring posttranslational modification of chemokines and new dimension of immunoregulation.
  Blood, 112, 2648-2656.  
  19017990 T.R.Wuest, and D.J.Carr (2008).
Dysregulation of CXCR3 signaling due to CXCL10 deficiency impairs the antiviral response to herpes simplex virus 1 infection.
  J Immunol, 181, 7985-7993.  
17222184 H.Fernando, G.T.Nagle, and K.Rajarathnam (2007).
Thermodynamic characterization of interleukin-8 monomer binding to CXCR1 receptor N-terminal domain.
  FEBS J, 274, 241-251.  
17217910 M.R.Yeaman, N.Y.Yount, A.J.Waring, K.D.Gank, D.Kupferwasser, R.Wiese, A.S.Bayer, and W.H.Welch (2007).
Modular determinants of antimicrobial activity in platelet factor-4 family kinocidins.
  Biochim Biophys Acta, 1768, 609-619.  
17291188 S.J.Allen, S.E.Crown, and T.M.Handel (2007).
Chemokine: receptor structure, interactions, and antagonism.
  Annu Rev Immunol, 25, 787-820.  
17148615 D.Vergote, G.S.Butler, M.Ooms, J.H.Cox, C.Silva, M.D.Hollenberg, J.H.Jhamandas, C.M.Overall, and C.Power (2006).
Proteolytic processing of SDF-1alpha reveals a change in receptor specificity mediating HIV-associated neurodegeneration.
  Proc Natl Acad Sci U S A, 103, 19182-19187.  
16784240 K.Rajarathnam, G.N.Prado, H.Fernando, I.Clark-Lewis, and J.Navarro (2006).
Probing receptor binding activity of interleukin-8 dimer using a disulfide trap.
  Biochemistry, 45, 7882-7888.  
17024562 L.Rajagopalan, and K.Rajarathnam (2006).
Structural basis of chemokine receptor function--a model for binding affinity and ligand selectivity.
  Biosci Rep, 26, 325-339.  
16847335 R.A.Colvin, G.S.Campanella, L.A.Manice, and A.D.Luster (2006).
CXCR3 requires tyrosine sulfation for ligand binding and a second extracellular loop arginine residue for ligand-induced chemotaxis.
  Mol Cell Biol, 26, 5838-5849.  
15273303 V.Booth, I.Clark-Lewis, and B.D.Sykes (2004).
NMR structure of CXCR3 binding chemokine CXCL11 (ITAC).
  Protein Sci, 13, 2022-2028.
PDB code: 1rjt
15039444 V.Petkovic, C.Moghini, S.Paoletti, M.Uguccioni, and B.Gerber (2004).
Eotaxin-3/CCL26 is a natural antagonist for CC chemokine receptors 1 and 5. A human chemokine with a regulatory role.
  J Biol Chem, 279, 23357-23363.  
14730354 Y.Kise, S.W.Lee, S.G.Park, S.Fukai, T.Sengoku, R.Ishii, S.Yokoyama, S.Kim, and O.Nureki (2004).
A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 149-156.
PDB code: 1ulh
  12737818 G.J.Swaminathan, D.E.Holloway, R.A.Colvin, G.K.Campanella, A.C.Papageorgiou, A.D.Luster, and K.R.Acharya (2003).
Crystal structures of oligomeric forms of the IP-10/CXCL10 chemokine.
  Structure, 11, 521-532.
PDB codes: 1o7y 1o7z 1o80
12571234 G.S.Campanella, E.M.Lee, J.Sun, and A.D.Luster (2003).
CXCR3 and heparin binding sites of the chemokine IP-10 (CXCL10).
  J Biol Chem, 278, 17066-17074.  
12417585 I.Clark-Lewis, I.Mattioli, J.H.Gong, and P.Loetscher (2003).
Structure-function relationship between the human chemokine receptor CXCR3 and its ligands.
  J Biol Chem, 278, 289-295.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.